3RUC | pdb_00003ruc

Specific recognition of N-acetylated substrates and domain flexibility in WbgU: a UDP-GalNAc 4-epimerase

• PDB DOI: https://doi.org/10.2210/pdb3RUC/pdb

• Classification: ISOMERASE
• Organism(s): Plesiomonas shigelloides
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-05-04 Released: 2011-05-25 
• Deposition Author(s): Bhatt, V.S., Guan, W., Wang, P.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.270 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Specific recognition of N-acetylated substrates and domain flexibility in WbgU: a UDP-GalNAc 4-epimerase

Bhatt, V.S., Guan, W., Wang, P.G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 164.3 kDa 
• Atom Count: 11,405 
• Modeled Residue Count: 1,344 
• Deposited Residue Count: 1,404 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WbgU	A, B, C, D	351	Plesiomonas shigelloides	Mutation(s): 1  Gene Names: wbgU EC: 5.1.3.7
UniProt
Find proteins for Q7BJX9 (Plesiomonas shigelloides) Explore Q7BJX9  Go to UniProtKB:  Q7BJX9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], H [auth B], K [auth C], M [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
UD2	F [auth A], I [auth B], L [auth C], N [auth D]	URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE C17 H27 N3 O17 P2 LFTYTUAZOPRMMI-NESSUJCYSA-N
SO4	G [auth A], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.270 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.282	α = 90
b = 78.282	β = 90
c = 231.797	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-25 
Deposition Author(s): Bhatt, V.S., Guan, W., Wang, P.G.

Revision History  

• Version 1.0: 2011-05-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description